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Next-generation sequencing as source of SNP and structural variants information to improve breeding programs in Populus nigra

Abstract : Progress in applying new methods to forest tree breeding has understandably been slower because of the difficulty to acquire genomic data in the major commercial species. The situation has improved rapidly through whole genome sequencing in Populus trichocarpa, and the construction of large EST databases in poplar. Nevertheless, the genomic tools to develop molecular markers for advanced breeding are still not adequate, in particular for the native European poplar species, P. nigra. In the framework of a joint resequencing effort undertaken by the EU funded projects Evoltree, Noveltree and EnergyPoplar, we aim at producing a sequence-marker map made of SNPs, short InDels and copy number variants covering the whole black poplar genome by means of next generation sequencing. First, by using the Illumina/Solexa technology we resequenced three different European individuals at a coverage > 20X in order to obtain both SNP and structural variants information and a draft sequence for the black poplar genome. Pilot analyses showed the feasibility of using P. trichocarpa genome sequence as reference for P. nigra, given that 75% of P. nigra reads were uniquely mapped on the P. trichocarpa sequence. We will present data on types and frequency of sequence variants at the whole genome level based on the sequences of the three individuals. Then, to maximize SNP discovery all over the genome, sequence reads obtained from 50 additional European clones, which have been resequenced at 2X coverage, will be aligned to the black poplar draft consensus sequence. Such SNP detection will be supported and confirmed by P. nigra sequences of several gene fragments, which were resequenced in different natural European populations by using the traditional Sanger method. The final SNPs data will be used for high throughput genotyping of an association population made of 1100 poplar clones established in two experimental sites, in order to monitor genetic variation during the selection process and develop Marker-Assisted-Selection and Gene-Assisted-Selection breeding programs.
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  • HAL Id : hal-02755743, version 1
  • PRODINRA : 48221



Stefania Giacomello, Giusi Zaina, Fabio Marroni, Sara Pinosio, Cristian del Fabbro, et al.. Next-generation sequencing as source of SNP and structural variants information to improve breeding programs in Populus nigra. 5. International Poplar Symposium;IPS V, Sep 2010, Orvieto, Italy. ⟨hal-02755743⟩



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